Update for backend behaviour changes

src/scitacean/datablock.py

@@ -31,10 +31,10 @@ class OrigDatablock:
 
     _files: List[File] = dataclasses.field(init=False)
     checksum_algorithm: Optional[str] = None
-    access_groups: Optional[List[str]] = None
     instrument_group: Optional[str] = None
     owner_group: Optional[str] = None
     init_files: dataclasses.InitVar[Optional[Iterable[File]]] = None
+    _access_groups: Optional[List[str]] = None
     _created_at: Optional[datetime] = None
     _created_by: Optional[str] = None
     _dataset_id: Optional[PID] = None
@@ -67,8 +67,8 @@ def from_download_model(
         return OrigDatablock(
             checksum_algorithm=dblock.chkAlg,
             owner_group=dblock.ownerGroup,
-            access_groups=dblock.accessGroups,
             instrument_group=dblock.instrumentGroup,
+            _access_groups=dblock.accessGroups,
             _created_at=dblock.createdAt,
             _created_by=dblock.createdBy,
             _dataset_id=orig_datablock_model.datasetId,
@@ -92,6 +92,11 @@ def size(self) -> int:
         """Total size of all files."""
         return sum(file.size for file in self.files)
 
+    @property
+    def access_groups(self) -> Optional[List[str]]:
+        """Access groups for this datablock."""
+        return self._access_groups
+
     @property
     def created_at(self) -> Optional[datetime]:
         """Creation time of this orig datablock."""

src/scitacean/testing/client.py

@@ -238,10 +238,10 @@ def create_orig_datablock(
         self, dblock: model.UploadOrigDatablock
     ) -> model.DownloadOrigDatablock:
         """Create a new orig datablock in SciCat."""
-        ingested = _process_orig_datablock(dblock)
-        dataset_id = ingested.datasetId
-        if dataset_id not in self.main.datasets:
+        dataset_id = dblock.datasetId
+        if (dset := self.main.datasets.get(dataset_id)) is None:
             raise ScicatCommError(f"No dataset with id {dataset_id}")
+        ingested = _process_orig_datablock(dblock, dset)
         self.main.orig_datablocks.setdefault(dataset_id, []).append(ingested)
         return ingested
 
@@ -338,6 +338,7 @@ def _process_dataset(
 
 def _process_orig_datablock(
     dblock: model.UploadOrigDatablock,
+    dset: model.DownloadDataset,
 ) -> model.DownloadOrigDatablock:
     created_at = datetime.datetime.now(tz=datetime.timezone.utc)
     # TODO use user login if possible
@@ -347,6 +348,7 @@ def _process_orig_datablock(
     fields = _model_dict(dblock)
     if "dataFileList" in fields:
         fields["dataFileList"] = list(map(_process_data_file, fields["dataFileList"]))
+    fields["accessGroups"] = dset.accessGroups
     processed = model.construct(
         model.DownloadOrigDatablock,
         _strict_validation=False,
@@ -356,8 +358,6 @@ def _process_orig_datablock(
         updatedAt=created_at,
         **fields,
     )
-    if dblock.datasetId is not None:
-        processed.datasetId = dblock.datasetId
     return processed
 
 

tests/client/datablock_client_test.py

@@ -52,7 +52,6 @@ def orig_datablock(scicat_access):
         ],
         datasetId="PLACEHOLDER",
         ownerGroup=scicat_access.user.group,
-        accessGroups=["group1", "2nd_group"],
     )
 
 
@@ -74,9 +73,10 @@ def test_create_first_orig_datablock(scicat_client, derived_dataset, orig_databl
         # The database populates a number of fields that are orig_datablock in dset.
         # But we don't want to test those here as we don't want to test the database.
         if expected is not None and key != "dataFileList":
-            assert expected == dict(downloaded)[key], f"key = {key}"
+            assert dict(downloaded)[key] == expected, f"key = {key}"
+    assert downloaded.accessGroups == derived_dataset.accessGroups
     for i in range(len(orig_datablock.dataFileList)):
         for key, expected in orig_datablock.dataFileList[i]:
             assert (
-                expected == dict(downloaded.dataFileList[i])[key]
+                dict(downloaded.dataFileList[i])[key] == expected
             ), f"i = {i}, key = {key}"

tests/client/sample_client_test.py

@@ -10,6 +10,32 @@
 from scitacean.model import (
     Sample,
 )
+from scitacean.testing.backend import config as backend_config
+from scitacean.testing.backend import skip_if_not_backend
+
+
+# Creating samples requires at least ingestor permissions.
+@pytest.fixture()
+def ingestor_access(
+    scicat_access: backend_config.SciCatAccess,
+) -> backend_config.SciCatAccess:
+    return backend_config.SciCatAccess(
+        url=scicat_access.url,
+        user=backend_config.USERS["ingestor"],
+    )
+
+
+@pytest.fixture()
+def real_client(
+    request: pytest.FixtureRequest,
+    ingestor_access: backend_config.SciCatAccess,
+    scicat_backend: bool,
+) -> Client:
+    skip_if_not_backend(request)
+    return Client.from_credentials(
+        url=ingestor_access.url,
+        **ingestor_access.user.credentials,
+    )
 
 
 @pytest.fixture()
@@ -18,12 +44,13 @@ def scicat_client(client: Client) -> ScicatClient:
 
 
 @pytest.fixture()
-def sample(scicat_access):
+def sample(ingestor_access):
+    scicat_access = ingestor_access
     return Sample(
         owner_group=scicat_access.user.group,
         access_groups=["group1", "2nd_group"],
         description="A test sample for Scitacean",
-        owner="ridcully",
+        owner=scicat_access.user.username,
         sample_characteristics={"layers": ["H2O", "EtOH"], "mass": 2},
     )